DBNascent | Samples

SRZ2961006 Sample ID 1774

**Data sources**
Paper identifier	Magnuson2015identifying
SRP accession	SRP066673
GEO accession	GSE75398
Samples	SRR2961006
	SRR2961007

**Technical details**
QC score	4
Replicate	1
Protocol	Bru-seq
Library prep	ligation
Spike-in	None
Single/Paired end	single
Raw strandedness	reverse
Reverse complemented?	True
Mapped strandedness	forward
Timecourse	False
Control/Experimental	experimental
Wildtype & Untreated?	False
Outlier	No
Unusable	No

**Downloads**
TDF visualization file	TDF file	57 Mb
Stranded gene read counts	TXT file	1 Mb
Unstranded bidirectional read counts	TXT file	21 Mb
Tfit bidirectional regions	BED file	1 Mb
dREG bidirectional regions	BED file	386 Kb
All data files	ZIP archive

**Cellular details**
Organism	H. sapiens
Sample type	cell line
Cell type	HF1
Clone/Individual
Strain
Genotype
Construct

**Conditions and treatments**
Condition type	Treatment	Start time	End time	Duration
treatment	bromouridine (2 mM)	-30 min	0 min	30 min
treatment	ultraviolet C (1 J/m^2/s)	-1820 s	-1800 s	20 s
treatment	TNF-alpha (10 ng/mL)	-90 min	-30 min	1 hr

**Extended notes**
Pipeline info and software versions
Sample notes	Bru-seq; replicate information unclear, but points toward technical replicates
Analysis notes

**Sample metrics**
Sample QC score	4
Sample NRO score	2
Raw read length	52
Read depth after trimming	53,335,926
Duplication proportion	0.87091
Proportion reads mapped	0.9419
Exon/intron ratio	2.91734
Unique read proportion	0.31666

**Bidirectionals**
Total # Tfit bidirectionals	13448
# Promoter Tfit bidirectionals	2563
# Intronic Tfit bidirectionals	8384
# Intergenic Tfit bidirectionals	1915
Total # dREG bidirectionals	8915
# Promoter dREG bidirectionals	2049
# Intronic dREG bidirectionals	5570
# Intergenic dREG bidirectionals	1434
Part of Tfit master merge?	True
Part of dREG master merge?	True